“A Shiny App for R-Package Risk Assessment”

Lars Andersen, 21st July 2023 @useR!2023 Basel

Disclaimer




Any opinions expressed in this presentation and on the following slides are solely those of the presenter and do not necessarily reflect those of BI

Validating open-source software

  • Consortia of ~50 companies (mostly pharma and biotech)
  • Mission: R Validation Hub is a cross-industry initiative whose mission is to enable the use of R by the Bio-Pharmaceutical industry in a regulatory setting, where the output may be used in submissions to regulatory agencies.

Two tools and what do they do?



is a framework to quantify an R package’s “risk” by assessing several meaningful metrics designed to evaluate package development best practices, code documentation, community engagement, and development sustainability.

is a full-fledged R package containing a shiny front-end that augments the utility of riskmetric. The application’s goal is to provide a central hub for an organization to review and assess the risk of R packages, providing handy tools and guide rails along the way.

Quantify risk programmatically

  • A license
  • Source code available for browsing
  • An easy to contact maintainer
  • A place to report bugs
  • Evidence that new bugs are being addressed
  • Complete Function documentation
  • Adequate test coverage
  • Community usage
  • Many more!

Why create a Shiny app?

  • Analyze riskmetric output without the need to write R code
  • Run riskmetric on the same machine with the same environment – creating central hub for reproducibility of risk scores
  • Facilitate and store communication on certain packages / metrics
  • Automatic package categorization with an overall decision based on riskmetric scores
  • Generate dynamic reports
  • Leverage user authentication with user role management

Demo

Coming soon

  • riskscore

in it’s early stages, a new data package the R Validation Hub is working on, that contains the riskmetric scores for all pkgs on CRAN.

  • Package Explorer

include GSK’s code to manually navigate the actual package contents (e.g. browse the robustness of tests written for each function).

Team

Q & A